List of files:
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README	-> This file

Binding modes are scored using their FullFitness and clustered. Clusters are
then rankied according to the average FullFitness of their elements
(see Grosdidier et. al., Proteins. 2007 Jun 1;67(4):1010-25).
The RMSD to reference is calculated between a predicted binding mode and the initial
position, orientation and conformation of the ligand. This is relevant ONLY
if you carefully placed your ligand as you expect prior to starting the docking
asssay.

1. PDB and DOCK4 files
----------------------

These are PDB files that can be used with your favorite program:

  clusters.dock4.pdb
  target.pdb

For instance, predicted poses can be displayed easily with UCSF Chimera [1]:
1. File > Open , then load target.pdb
2. Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format)

The PDB for all individual predicted poses can be generated by splitting the clusters.dock4.pdb.


2. CHARMM input files
---------------------

These are files that can be used with CHARMM [2].

  complex.psf	: protein structure file (PSF) for the complex
  complex.crd	: coordinate file (CRD) for the reference complex
  target.crd	: coordinate file (CRD) for the target protein alone
  test.inp	: sample CHARMM input file

  merged.par	: extra parameter file (if needed)
  merged.rtf	: extra topology file (if needed)

  clusters.zip	: zipped CRD files for the predicted binding modes

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The SwissDock team.

[1] http://www.cgl.ucsf.edu/chimera/
[2] http://www.charmm.org
